# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 13:55:03 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (2S)-1-[1-(4-phenylbutanoyl)-L-prolyl]pyrrolidine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCCc1ccccc1)N2CCC[C@H]2C(=O)N3CCC[C@H]3C#N
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 2P6  2P6  (2S)-1-[1-(4-phenylbutanoyl)-L-prolyl]pyrrolidine-2-carbonitrile  ligand  50  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2P6
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 2P6  C17   C  CH2   0  -0.601  -1.5821   1.2381   0.3813
 2P6  C18   C  CH2   0  -0.405  -2.7590   0.3997  -0.0900
 2P6  C19   C  CH2   0  -0.507  -4.0649   0.8562   0.5637
 2P6  C20   C  CR6   0   0.138  -5.2338   0.0144   0.1347
 2P6  C21   C  CR16  0  -0.308  -5.4659  -1.2269   0.7256
 2P6  C25   C  CR16  0  -0.319  -6.0852   0.4300  -0.8866
 2P6  C22   C  CR16  0  -0.240  -6.5177  -2.0308   0.3086
 2P6  C24   C  CR16  0  -0.239  -7.1404  -0.3700  -1.3074
 2P6  C23   C  CR16  0  -0.275  -7.3595  -1.6049  -0.7117
 2P6  C15   C  C     0   0.573  -0.2648   0.8387  -0.2435
 2P6  O16   O  O     0  -0.505  -0.1467  -0.1363  -0.9756
 2P6  N14   N  NT    0  -0.464   0.7884   1.6265   0.0426
 2P6  C10   C  CH1   0  -0.226   2.0984   1.3091  -0.4731
 2P6  C8    C  C     0   0.594   2.6557   0.0724   0.2244
 2P6  O9    O  O     0  -0.479   2.2120  -0.3253   1.2894
 2P6  C11   C  CH2   0  -0.468   2.9206   2.5576  -0.1213
 2P6  C12   C  CH2   0  -0.482   2.2794   3.0392   1.1759
 2P6  C13   C  CH2   0  -0.264   0.7952   2.7536   0.9694
 2P6  C1    C  CSP   0   0.133   4.7986  -1.3811   1.6289
 2P6  N2    N  NS    0  -0.266   5.2231  -1.1747   2.6776
 2P6  C3    C  CH1   0  -0.130   4.3179  -1.6888   0.2797
 2P6  C4    C  CH2   0  -0.480   5.4735  -2.0711  -0.6594
 2P6  C5    C  CH2   0  -0.477   4.9970  -1.5560  -2.0110
 2P6  C6    C  CH2   0  -0.279   4.3133  -0.2435  -1.6581
 2P6  N7    N  NT    0  -0.500   3.7087  -0.5321  -0.3592
 2P6  H17   H  HCH2  0   0.265  -1.7661   2.2987   0.1791
 2P6  H17A  H  HCH2  0   0.269  -1.4846   1.1643   1.4706
 2P6  H18   H  HCH2  0   0.232  -2.8576   0.4651  -1.1761
 2P6  H18A  H  HCH2  0   0.233  -2.5875  -0.6534   0.1445
 2P6  H19   H  HCH2  0   0.239  -3.9572   0.8094   1.6513
 2P6  H19A  H  HCH2  0   0.240  -4.2484   1.9042   0.3127
 2P6  H21   H  HCR6  0   0.244  -4.8168  -1.5682   1.5245
 2P6  H25   H  HCR6  0   0.245  -5.9237   1.3940  -1.3554
 2P6  H22   H  HCR6  0   0.252  -6.6817  -2.9911   0.7810
 2P6  H24   H  HCR6  0   0.252  -7.7922  -0.0264  -2.1009
 2P6  H23   H  HCR6  0   0.252  -8.1803  -2.2301  -1.0387
 2P6  H10   H  HCH1  0   0.292   2.0574   1.1533  -1.5523
 2P6  H11   H  HCH2  0   0.264   3.9876   2.3565  -0.0255
 2P6  H11A  H  HCH2  0   0.263   2.7944   3.2984  -0.9122
 2P6  H12   H  HCH2  0   0.247   2.6598   2.4713   2.0259
 2P6  H12A  H  HCH2  0   0.261   2.4681   4.0935   1.3714
 2P6  H13   H  HCH2  0   0.245   0.2824   3.6151   0.5326
 2P6  H13A  H  HCH2  0   0.254   0.2925   2.5041   1.9044
 2P6  H3    H  HCH1  0   0.329   3.5967  -2.5070   0.3690
 2P6  H4A   H  HCH2  0   0.282   5.6630  -3.1418  -0.6363
 2P6  H5    H  HCH2  0   0.269   5.8138  -1.4187  -2.7172
 2P6  H5A   H  HCH2  0   0.255   4.2770  -2.2457  -2.4548
 2P6  H6    H  HCH2  0   0.254   5.0369   0.5718  -1.5787
 2P6  H6A   H  HCH2  0   0.271   3.5594   0.0373  -2.3915
 2P6  H4    H  HCH2  0   0.266   6.3881  -1.5571  -0.3610

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 2P6  C1   N2    triple    1.150  0.020  1.150
 2P6  C1   C3    single    1.465  0.020  1.465
 2P6  C3   C4    single    1.537  0.020  1.537
 2P6  C3   N7    single    1.455  0.020  1.455
 2P6  C4   C5    single    1.523  0.020  1.523
 2P6  C5   C6    single    1.521  0.020  1.521
 2P6  C6   N7    single    1.461  0.020  1.461
 2P6  N7   C8    single    1.347  0.020  1.347
 2P6  C8   O9    double    1.220  0.020  1.220
 2P6  C8   C10   single    1.525  0.020  1.525
 2P6  C10  C11   single    1.536  0.020  1.536
 2P6  C10  N14   single    1.443  0.020  1.443
 2P6  C11  C12   single    1.525  0.020  1.525
 2P6  C12  C13   single    1.525  0.020  1.525
 2P6  C13  N14   single    1.459  0.020  1.459
 2P6  N14  C15   single    1.346  0.020  1.346
 2P6  C15  O16   double    1.225  0.020  1.225
 2P6  C15  C17   single    1.512  0.020  1.512
 2P6  C17  C18   single    1.520  0.020  1.520
 2P6  C18  C19   single    1.530  0.020  1.530
 2P6  C19  C20   single    1.503  0.020  1.503
 2P6  C20  C21   aromatic  1.394  0.020  1.394
 2P6  C20  C25   aromatic  1.393  0.020  1.393
 2P6  C21  C22   aromatic  1.388  0.020  1.388
 2P6  C22  C23   aromatic  1.390  0.020  1.390
 2P6  C23  C24   aromatic  1.388  0.020  1.388
 2P6  C24  C25   aromatic  1.389  0.020  1.389
 2P6  C3   H3    single    0.970  0.020  1.090
 2P6  C4   H4    single    0.970  0.020  1.090
 2P6  C4   H4A   single    0.970  0.020  1.090
 2P6  C5   H5    single    0.970  0.020  1.090
 2P6  C5   H5A   single    0.970  0.020  1.090
 2P6  C6   H6    single    0.970  0.020  1.090
 2P6  C6   H6A   single    0.970  0.020  1.090
 2P6  C10  H10   single    0.970  0.020  1.090
 2P6  C11  H11   single    0.970  0.020  1.090
 2P6  C11  H11A  single    0.970  0.020  1.090
 2P6  C12  H12   single    0.970  0.020  1.090
 2P6  C12  H12A  single    0.970  0.020  1.090
 2P6  C13  H13   single    0.970  0.020  1.090
 2P6  C13  H13A  single    0.970  0.020  1.090
 2P6  C17  H17   single    0.970  0.020  1.090
 2P6  C17  H17A  single    0.970  0.020  1.090
 2P6  C18  H18   single    0.970  0.020  1.090
 2P6  C18  H18A  single    0.970  0.020  1.090
 2P6  C19  H19   single    0.970  0.020  1.090
 2P6  C19  H19A  single    0.970  0.020  1.090
 2P6  C21  H21   single    0.930  0.020  1.080
 2P6  C22  H22   single    0.930  0.020  1.080
 2P6  C23  H23   single    0.930  0.020  1.080
 2P6  C24  H24   single    0.930  0.020  1.080
 2P6  C25  H25   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 2P6  H17A  C17  H17  105.29  3.000
 2P6  H17A  C17  C15  108.39  3.000
 2P6  H17   C17  C15  109.02  3.000
 2P6  H17A  C17  C18  109.87  3.000
 2P6  H17   C17  C18  110.29  3.000
 2P6  C15   C17  C18  113.63  3.000
 2P6  H18A  C18  H18  106.57  3.000
 2P6  H18A  C18  C19  109.26  3.000
 2P6  H18   C18  C19  109.26  3.000
 2P6  H18A  C18  C17  110.10  3.000
 2P6  H18   C18  C17  110.19  3.000
 2P6  C19   C18  C17  111.34  3.000
 2P6  H19A  C19  H19  106.61  3.000
 2P6  H19A  C19  C20  109.93  3.000
 2P6  H19   C19  C20  109.66  3.000
 2P6  H19A  C19  C18  109.34  3.000
 2P6  H19   C19  C18  109.14  3.000
 2P6  C20   C19  C18  112.01  3.000
 2P6  C25   C20  C21  118.33  3.000
 2P6  C25   C20  C19  121.17  3.000
 2P6  C21   C20  C19  120.47  3.000
 2P6  H21   C21  C22  119.51  3.000
 2P6  H21   C21  C20  119.52  3.000
 2P6  C22   C21  C20  120.97  3.000
 2P6  H25   C25  C24  119.61  3.000
 2P6  H25   C25  C20  119.42  3.000
 2P6  C24   C25  C20  120.96  3.000
 2P6  H22   C22  C23  120.03  3.000
 2P6  H22   C22  C21  119.83  3.000
 2P6  C23   C22  C21  120.14  3.000
 2P6  H24   C24  C23  120.11  3.000
 2P6  H24   C24  C25  119.76  3.000
 2P6  C23   C24  C25  120.13  3.000
 2P6  H23   C23  C24  120.25  3.000
 2P6  H23   C23  C22  120.28  3.000
 2P6  C24   C23  C22  119.48  3.000
 2P6  N14   C15  O16  121.16  3.000
 2P6  O16   C15  C17  122.78  3.000
 2P6  N14   C15  C17  116.06  3.000
 2P6  C13   N14  C10  113.12  3.000
 2P6  C13   N14  C15  126.21  3.000
 2P6  C10   N14  C15  120.36  3.000
 2P6  H10   C10  C11  111.27  3.000
 2P6  H10   C10  C8   110.50  3.000
 2P6  C11   C10  C8   111.02  3.000
 2P6  H10   C10  N14  110.53  3.000
 2P6  C11   C10  N14  103.02  3.000
 2P6  C8    C10  N14  110.28  3.000
 2P6  N7    C8   O9   121.06  3.000
 2P6  O9    C8   C10  122.04  3.000
 2P6  N7    C8   C10  116.83  3.000
 2P6  H11A  C11  H11  107.59  3.000
 2P6  H11A  C11  C12  110.70  3.000
 2P6  H11   C11  C12  113.27  3.000
 2P6  H11A  C11  C10  108.90  3.000
 2P6  H11   C11  C10  113.22  3.000
 2P6  C12   C11  C10  103.09  3.000
 2P6  H12A  C12  H12  107.68  3.000
 2P6  H12A  C12  C13  111.98  3.000
 2P6  H12   C12  C13  110.32  3.000
 2P6  H12A  C12  C11  112.69  3.000
 2P6  H12   C12  C11  110.60  3.000
 2P6  C13   C12  C11  103.58  3.000
 2P6  H13A  C13  H13  107.85  3.000
 2P6  H13A  C13  C12  112.05  3.000
 2P6  H13   C13  C12  111.27  3.000
 2P6  H13A  C13  N14  111.45  3.000
 2P6  H13   C13  N14  110.64  3.000
 2P6  C12   C13  N14  103.60  3.000
 2P6  C3    C1   N2   180.00  3.000
 2P6  H3    C3   N7   110.75  3.000
 2P6  H3    C3   C4   111.06  3.000
 2P6  N7    C3   C4   104.13  3.000
 2P6  H3    C3   C1   107.35  3.000
 2P6  N7    C3   C1   112.01  3.000
 2P6  C4    C3   C1   111.60  3.000
 2P6  H4A   C4   H4   108.18  3.000
 2P6  H4A   C4   C5   113.98  3.000
 2P6  H4    C4   C5   110.23  3.000
 2P6  H4A   C4   C3   111.27  3.000
 2P6  H4    C4   C3   110.25  3.000
 2P6  C5    C4   C3   102.87  3.000
 2P6  H5A   C5   H5   108.12  3.000
 2P6  H5A   C5   C6   110.07  3.000
 2P6  H5    C5   C6   112.27  3.000
 2P6  H5A   C5   C4   110.70  3.000
 2P6  H5    C5   C4   112.56  3.000
 2P6  C6    C5   C4   103.09  3.000
 2P6  H6A   C6   H6   108.37  3.000
 2P6  H6A   C6   N7   111.30  3.000
 2P6  H6    C6   N7   110.90  3.000
 2P6  H6A   C6   C5   112.17  3.000
 2P6  H6    C6   C5   111.27  3.000
 2P6  N7    C6   C5   102.81  3.000
 2P6  C6    N7   C3   111.97  3.000
 2P6  C6    N7   C8   128.30  3.000
 2P6  C3    N7   C8   119.58  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 2P6  CONST_01  C23  C22  C21  C20     0.00   0.0  0
 2P6  CONST_02  C23  C24  C25  C20     0.00   0.0  0
 2P6  CONST_03  C24  C25  C20  C21     0.00   0.0  0
 2P6  CONST_04  C24  C23  C22  C21     0.00   0.0  0
 2P6  CONST_05  C22  C21  C20  C25     0.00   0.0  0
 2P6  CONST_06  C22  C23  C24  C25     0.00   0.0  0
 2P6  CONST_07  C22  C21  C20  C19   180.00   0.0  0
 2P6  CONST_08  C24  C25  C20  C19   180.00   0.0  0
 2P6  CONST_09  C3   N7   C8   C10   180.00   0.0  0
 2P6  CONST_10  C6   N7   C8   C10     0.00   0.0  0
 2P6  CONST_11  H22  C22  C21  C20   180.00   0.0  0
 2P6  CONST_12  H24  C24  C25  C20   180.00   0.0  0
 2P6  CONST_13  H25  C25  C20  C21   180.00   0.0  0
 2P6  CONST_14  H23  C23  C22  C21   180.00   0.0  0
 2P6  CONST_15  H21  C21  C20  C25   180.00   0.0  0
 2P6  CONST_16  C10  N14  C15  C17   180.00   0.0  0
 2P6  CONST_17  C13  N14  C15  C17     0.00   0.0  0
 2P6  CONST_18  C10  N14  C15  O16     0.00   0.0  0
 2P6  CONST_19  C13  N14  C15  O16   180.00   0.0  0
 2P6  CONST_20  C3   N7   C8   O9      0.00   0.0  0
 2P6  CONST_21  C6   N7   C8   O9    180.00   0.0  0
 2P6  Var_01    C11  C12  C13  N14    27.58  30.0  1
 2P6  Var_02    C13  C12  C11  C10   -36.88  30.0  1
 2P6  Var_03    C12  C13  N14  C10    -7.68  30.0  1
 2P6  Var_04    C6   C5   C4   C3     38.37  30.0  1
 2P6  Var_05    C5   C6   N7   C3     19.02  30.0  1
 2P6  Var_06    N7   C6   C5   C4    -35.18  30.0  1
 2P6  Var_07    C21  C20  C19  C18    80.45  30.0  2
 2P6  Var_08    C20  C19  C18  C17  -178.55  30.0  3
 2P6  Var_09    N14  C15  C17  C18   174.03  30.0  1
 2P6  Var_10    C15  C17  C18  C19  -179.47  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2P6  chir_01  C10  C8  C11  N14  positiv
 2P6  chir_02  C3   N7  C4   C1   negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 2P6  plan-1  C17  0.020
 2P6  plan-1  C15  0.020
 2P6  plan-1  O16  0.020
 2P6  plan-1  N14  0.020
 2P6  plan-1  C10  0.020
 2P6  plan-1  C13  0.020
 2P6  plan-2  C19  0.020
 2P6  plan-2  C20  0.020
 2P6  plan-2  C21  0.020
 2P6  plan-2  C25  0.020
 2P6  plan-2  C22  0.020
 2P6  plan-2  C24  0.020
 2P6  plan-2  C23  0.020
 2P6  plan-2  H21  0.020
 2P6  plan-2  H25  0.020
 2P6  plan-2  H22  0.020
 2P6  plan-2  H24  0.020
 2P6  plan-2  H23  0.020
 2P6  plan-3  C10  0.020
 2P6  plan-3  C8   0.020
 2P6  plan-3  O9   0.020
 2P6  plan-3  C3   0.020
 2P6  plan-3  C6   0.020
 2P6  plan-3  N7   0.020

